Doctors Without Borders was only six years old in 1977 when one of its physicians first broke the organization’s rules against taking sides or bearing witness by denouncing Cambodia’s Khmer Rouge for exterminating its people.

Here was the humanitarian’s dilemma: Do you keep your mouth shut so you can help the victims? Or do you denounce the abusers and lose access to those who need you most?

For 40 years, the organi­zation, which has been awarded the Nobel Prize for its courageous work in war zones and in places devastated by catastrophes, has tried to have it both ways. At first, the choices were fairly easy. Because 90 percent of the world’s displaced people were fleeing militant socialist governments, relief groups during the cold war shared the same ideological agenda as the Western democracies in which they were based.

When the Soviet Union fell, it was seen “as a fantastic opportunity” to crusade for human rights, says Fabrice Weissman, research director of the MSF Foundation (the organization is known by the initials of its French name, Médicins Sans Frontières). But then the politics got muddier. “Aid came to be considered not as humanitarian relief, but to serve a political agenda in nation-building projects,” Weissman says. As MSF tried to steer a neutral course, it found that “one side thinks of you as leftist hippies,” while “the other thinks of you as colonial imperialists.” In 2004, MSF left Afghanistan after five of its aid workers were murdered, ostensibly by the Taliban. The killers had been identified, but the government did nothing to prosecute them.

With humanitarian workers being manipulated or scorned from all sides, it seemed to aid groups that opportunities to provide assistance were disappearing. But MSF believed that opportunities still existed, saying it would negotiate with criminals and even sometimes ignore their wrongdoing if doing so enabled aid workers to save lives.

The boldest statement of that philosophy appeared last year when MSF published Humanitarian Negotiations Revealed, a self-exposé disclosing that MSF paid an Al Qaeda-affiliated militia a $10,000-per-project registration fee to continue working in Somalia. And, to remain in Yemen, MSF had to apologize to the government for (deservedly) listing Yemen as one of 2009’s top ten humanitarian crises.

Perhaps more surprisingly, the disclosures haven’t caused donors to withhold funding or enraged governments, guerrillas and other belligerents. Instead, “it’s been very positive,” Weissman says. “People understand us better.” If anything, the transparency has helped the group by dispelling suspicion that it has a hidden agenda.

Other aid groups are less shy about advocacy. “We’ll be political when other organizations won’t,” says Shannon Scribner, humanitarian policy manager for Oxfam America. Still, she adds, her group always weighs the consequences. “Are you saving more lives by staying and not speaking out?”

MSF usually stays. In 2009, it returned to Afghanistan by opening one project in a government-controlled area and another in a Taliban stronghold. Both sides tolerated MSF because they claim it demonstrated their concern for local populations.

“Independence is a myth,” Weissman says. “Instead, we choose our dependencies. The only independence we have is the independence of mind.”